Eric Westhof - Academia.edu (original) (raw)

Papers by Eric Westhof

Acta Crystallographica, Aug 28, 2016

The packaging of eukaryotic DNA into chromatin consists of the nucleosome as the basic repeating ... more The packaging of eukaryotic DNA into chromatin consists of the nucleosome as the basic repeating unit. The nucleosome has a core region, comprised of ~146 base pairs of DNA wrapped around a protein octamer of core histones, in addition to a variable length of linker DNA. The linker DNA connecting adjacent nucleosome core regions is on average ~50 base pairs in length in higher eukaryotes and can be occupied by a linker histone. By modulating chromatin structure, dynamics and recognition by other nuclear factors, the core and linker histones regulate genomic function. The first atomic model of the nucleosome core (particle) was published in 1997 [1], paving the way for the structural solution of a great variety of nucleosome core constructs composed of variant/modified histones and different DNA sequences [2,3]. This has consequently revolutionized our understanding of nucleosome activity, and yet 19 years later we are still lacking an atomic level understanding of how linker histones interact with nucleosomes. In mammals, there are 11 linker histone variants, which can display cell type and cellular status dependent expression, site-specific localization in the nucleus as well as specific interactions with different nuclear factors to foster gene-specific regulation. In addition, the linker histones can undergo an enormity of post-translational modifications that further expand the regulatory landscape. Nonetheless, the general function of the linker histones is largely that of compacting nucleosomes into condensed chromatin states, which are generally repressive to gene expression. An atomic model of the chromatosome, the minimal assembly of a nucleosome with a linker histone, could significantly advance our understanding of chromatin function, and we present here the first X-ray crystal structure of a chromatosome [4]. [

$Research paper thumbnail of Importance of potassium ions for ribosome structure and function revealed by long-wavelength X-ray diffraction$

Nature Communications, 2019

The ribosome, the largest RNA-containing macromolecular machinery in cells, requires metal ions n... more The ribosome, the largest RNA-containing macromolecular machinery in cells, requires metal ions not only to maintain its three-dimensional fold but also to perform protein synthesis. Despite the vast biochemical data regarding the importance of metal ions for efficient protein synthesis and the increasing number of ribosome structures solved by X-ray crystallography or cryo-electron microscopy, the assignment of metal ions within the ribosome remains elusive due to methodological limitations. Here we present extensive experimental data on the potassium composition and environment in two structures of functional ribosome complexes obtained by measurement of the potassium anomalous signal at the K-edge, derived from long-wavelength X-ray diffraction data. We elucidate the role of potassium ions in protein synthesis at the three-dimensional level, most notably, in the environment of the ribosome functional decoding and peptidyl transferase centers. Our data expand the fundamental knowl...

Nucleic Acids Research, 2016

Precise conversion of genetic information into proteins is essential to cellular health. However,... more Precise conversion of genetic information into proteins is essential to cellular health. However, a margin of error exists and is at its highest on the stage of translation of mRNA by the ribosome. Here we present three crystal structures of 70S ribosome complexes with messenger RNA and transfer RNAs and show that when a G•U base pair is at the first position of the codon-anticodon helix a conventional wobble pair cannot form because of inescapable steric clash between the guanosine of the A codon and the key nucleotide of decoding center adenosine 1493 of 16S rRNA. In our structure the rigid ribosomal decoding center, which is identically shaped for cognate or near-cognate tRNAs, forces this pair to adopt a geometry close to that of a canonical G•C pair. We further strengthen our hypothesis that spatial mimicry due either to base tautomerism or ionization dominates the translation infidelity mechanism.

Acta Crystallographica Section A Foundations and Advances, 2015

Zeitschrift für Naturforschung C, 1975

With the use of PMR the ribose conform ations have been studied in the tem perature range - 60 to... more With the use of PMR the ribose conform ations have been studied in the tem perature range - 60 to + 40 °C in ND3 solutions of adenosine (A), guanosine (G), inosine (I), xanthosine (X), purineriboside (P R), 2-am inopurineriboside (2am P R), N6-isopentenyladenosine (N6ipA), 8-bromo-adenosine (8-BrA), 8-bromoguanosine (8-BrG), formycin B (F), tubercidin (T), isopropylidene-adenosine (iA), and isopropylideneguanosine (iG). The analysis is based on the two-state S ⇄ N model of the ribose m oiety proposed by Altona and Sundaralingam . The compounds studied can be classified into two groups: 1. A, I, G, X, PR , 2am PR, N6ipA, and T show a small tem perature dependence of the S ⇄ N equilibrium and [ S ] ~ 0 .6 ; 2. 8-BrA, 8-BrG, and F have a stronger tem perature dependence and [S] ~ 0 .8 . W ithin these two groups the sim ilarities observed are greater than observed in the solid state. Some therm odynam ic conclusions about the S ⇄ N and the syn ⇄ anti equilibria are presented. The result...

Zeitschrift für Naturforschung C, 1973

Radical formation by irradiation with X-rays in single crystals of 1-methyluracil has been measur... more Radical formation by irradiation with X-rays in single crystals of 1-methyluracil has been measured using ESR-spectroscopy at 9.5 GHz and 35 GHz. When irradiating and measuring at 77 °K radicals characterized by hydrogen abstraction from the methyl group were found to be predominating. For the hyperfine splittings principal values of 8.5 G, 18.2 G, 30.5 G were found for both α-protons and 3.3 G, 2.4 G, 1.7 G for the N (1)-splitting. Pairs of abstraction radicals were also found under these conditions showing quintet splittings of about 10 G and anisotropic dipolar coupling. Average distances parallel to c of 6.3 Å and 6.5 Å were found for two types of pairs while those perpendicular to c were not analyzed in detail. Irradiating and measuring at room temperature an additional sextet pattern was found in the spectrum and attributed to a radical formed by addition of hydrogen at C (5). For the hyperfine splittings principal values of 8.1 G, 17.5 G, 30.0 G were found for the α-proton an...

Nucleic acids research, Jul 8, 2016

RBscore&NBench combines a web server, RBscore and a database, NBench. RBscore predicts RNA-/DNA-b... more RBscore&NBench combines a web server, RBscore and a database, NBench. RBscore predicts RNA-/DNA-binding residues in proteins and visualizes the prediction scores and features on protein structures. The scoring scheme of RBscore directly links feature values to nucleic acid binding probabilities and illustrates the nucleic acid binding energy funnel on the protein surface. To avoid dataset, binding site definition and assessment metric biases, we compared RBscore with 18 web servers and 3 stand-alone programs on 41 datasets, which demonstrated the high and stable accuracy of RBscore. A comprehensive comparison led us to develop a benchmark database named NBench. The web server is available on: http://ahsoka.u-strasbg.fr/rbscorenbench/.

Annual review of biophysics, Jan 22, 2017

Biological functions of RNA molecules are dependent upon sustained specific three-dimensional (3D... more Biological functions of RNA molecules are dependent upon sustained specific three-dimensional (3D) structures of RNA, with or without the help of proteins. Understanding of RNA structure is frequently based on 2D structures, which describe only the Watson-Crick (WC) base pairs. Here, we hierarchically review the structural elements of RNA and how they contribute to RNA 3D structure. We focus our analysis on the non-WC base pairs and on RNA modules. Several computer programs have now been designed to predict RNA modules. We describe the RNA-Puzzles initiative, which is a community-wide, blind assessment of RNA 3D structure prediction programs to determine the capabilities and bottlenecks of current predictions. The assessment metrics used in RNA-Puzzles are briefly described. The detection of RNA 3D modules from sequence data and their automatic implementation belong to the current challenges in RNA 3D structure prediction.

Science, 2016

Tie me up, cut me down Group II in trons are mobile genetic elements found in all domains of life... more Tie me up, cut me down Group II in trons are mobile genetic elements found in all domains of life. They are large ribozymes that can excise themselves from host RNA. Costa et al. determined the structure of an excised group II intron in its branched conformation. This conformation is comparable to the branched “lariat” seen during the splicing of nuclear RNA transcripts. The lariat conformation helps assemble the group II active site for the reverse splicing reaction. The lariat in spliceosomal splicing may also have a similar role in the second step of messenger RNA intron removal. Science , this issue p. 10.1126/science.aaf9258

F1000 - Post-publication peer review of the biomedical literature, 2003

Spinal muscular atrophy (SMA) is a common neurodegenerative disease that is caused by deletions o... more Spinal muscular atrophy (SMA) is a common neurodegenerative disease that is caused by deletions or loss-of-function mutations in the Survival of Motor Neuron (SMN) protein. SMN is part of a large complex that functions in the assembly/restructuring of ribonucleoprotein (RNP) complexes. We recently showed in HeLa cells that two components of the SMN complex, Gemin3 and Gemin4, together with the argonaute protein eIF2C2, also associate with microRNAs (miRNAs) as part of a novel class of RNPs termed miRNPs. Here we report on miRNPs isolated from neuronal cell lines of mouse and human, and describe 53 novel miRNAs. Several of these miRNAs are conserved in divergent organisms, including rat, zebrafish, pufferfish, and the nematode Caenorhabditis elegans. The chromosomal locations of most of the novel miRNAs were identified and indicate some phylogenetic conservation of the likely precursor structures. Interestingly the gene locus of one miRNA, miR-175, is a candidate region for two neurologic diseases: early-onset parkinsonism (Waisman syndrome) and X-linked mental retardation (MRX3). Also, several miRNAs identified as part of miRNPs in these cells appear to constitute two distinct subfamilies. These subfamilies comprise multiple copies of miRNAs on different chromosomes, suggesting an important function in the regulation of gene expression.

F1000 - Post-publication peer review of the biomedical literature, 2014

Nucleic acids symposium series (2004), 2005

Aminoglycosides are highly effective antibacterial drugs that decrease translation accuracy by bi... more Aminoglycosides are highly effective antibacterial drugs that decrease translation accuracy by binding to the aminoacyl-tRNA decoding site (A site) of 16S ribosomal RNA. On the other hand, they are highly toxic to mammals through kidney and ear-associated illnesses by binding to ribosomal A sites. To understand the mechanism of toxicity of aminoglycosides to mammals at atomic level, crystallographic studies have been carried out with a number of Homo sapiens mitochondrial and cytoplasmic A sites complexed with aminoglycosides. Several X-ray diffraction data sets were successfully collected. Initial phases of mitochondrial A site with tobramycin and cytoplasmic A site with paromomycin were derived by the molecular replacement method. Refinements of atomic parameters are now under progress.

RNA (New York, N.Y.), 1997

A portion of the 3'UTR of the human transferrin receptor mRNA mediates iron-dependent regulat... more A portion of the 3'UTR of the human transferrin receptor mRNA mediates iron-dependent regulation of mRNA stability. The minimal RNA regulatory region contains three conserved hairpins, so-called iron responsive elements (IREs), that are recognized specifically by iron regulatory proteins (IRPs). The structure of this regulatory region and its complex with IRP-1 was probed using a combination of enzymes and chemicals. The data support the existence of an intrinsic IRE loop structure that is constrained by an internal C-G base pair. This particular structure is one of the determinants required for optimal IRP binding. IRP-1 covers one helical turn of the IRE and protects conserved residues in each of the three IREs: the bulged cytosine and nucleotides in the hairpin loops. Two essential IRP-phosphate contacts were identified by ethylation interference. Three-dimensional modeling of one IRE reveals that IRP-1 contacts several bases and the ribose-phosphate backbone located on one f...

RNA (New York, N.Y.), 1996

Binding of Escherichia coli and Thermus thermophilus ribosomal proteins S15 to a 16S ribosomal RN... more Binding of Escherichia coli and Thermus thermophilus ribosomal proteins S15 to a 16S ribosomal RNA fragment from T. thermophilus (nt 559-753) has been investigated in detail by extensive deletion analysis, filter-binding assays, gel mobility shift, structure probing, footprinting with chemical, enzymatic, and hydroxyl radical probes. Both S15 proteins recognize two distinct sites. The first one maps in the bottom of helix 638-655/717-734 (H22) and in the three-way junction between helix 560-570/737-747 (H20), helix 571-600/606-634 (H21), and H22. The second is located in a conserved purine-rich region in the center of H22. The first site provides a higher contribution to the free energy of binding than the second one, and both are required for efficient binding. A short RNA fragment of 56 nt containing these elements binds S15 with high affinity. The structure of the rRNA is constrained by the three-way junction and requires both magnesium and S15 to be stabilized. A 3D model, deriv...

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, 2005

A computer-based approach to the modeling of the architecture of RNA molecules is described. It e... more A computer-based approach to the modeling of the architecture of RNA molecules is described. It exploits the available crystal structures, sequences, and analyzing tools. The method is anchored in our understanding of the physicochemical processes that RNA molecules undergo when folding into their three-dimensional structures. The folding is sequential, with modular units being incorporated hierarchically in the final architecture. The aim is to assemble a folded architecture of a structured RNA from known modules and known interaction motifs in order to suggest further experimental work about new contacts or new folding units. Although large RNA molecules are built using all-atom components, the atomic details cannot, in most regions, be deduced with confidence. Keywords: RNA; molecular modeling; RNA motif; secondary structure; tertiary structure; RNA architecture

Applications, Theory and Instrumentation, 2000

Abbreviations and Acronyms 9 Related Articles 9 References 9 Ribonucleic acids are negatively cha... more Abbreviations and Acronyms 9 Related Articles 9 References 9 Ribonucleic acids are negatively charged polymers assembled from four different types of monomers. Each monomer is made of an invariant phosphorylated sugar to which is attached one of the four standard nucleic acid bases; the pyrimidines uracil and cytosine, and the purines guanine and adenine. The first level of organization is thus the sequence of bases attached to the sugar-phosphate backbone. In salty water, the RNA molecules fold back on themselves via Watson-Crick base pairing between the bases (A with U, G with C or U) leading to double-stranded helices interrupted by single-stranded regions in internal loops or hairpin loops. The enumeration of the base-paired regions or helices constitutes a description of the second level of organization, the secondary structure. The methods available to deduce the secondary structure of an RNA molecule are mainly of three types: the phylogenetic approach, the theoretical prediction, and chemical/enzymatic methods. The secondary structure of an RNA molecule is experimentally accessible and its content measurable. Under appropriate conditions, structured RNA molecules undergo a transition to a three-dimensional (3D) fold in which the helices and the unpaired regions are precisely organized in space. This folding process usually depends on the presence of divalent ions, such as magnesium ions, and on the temperature. The tertiary structure is the level of organization relevant for biological function of structured RNA molecules.